`

MgRNA: Classification of Mg2+ binding sites in RNA crystal structures

Back to Classification Home Download this subset in: CSV, XML, JSON
Representative site 1vs7:A1593, See in JSmolMgRNA representative site for type 2PO            Click on the image to toggle views


Site type: 2Pout

Schematic drawing for
2Pout

MgRNA type 2PO
List of all 191 Mg2+ binding sites with the site type 2Pout in RNA crystal structures in the benchmark dataset (switch to full dataset)
Sites in the table can be ordered by the following fields by clicking the column header: "PDB ID" or "Mg2+ ID"
Page 6 of 8 | | | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8
Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands
PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout
4bpn A5053 2Pout A6180, A6181, A6182, A6183, A6184, A6185 G:A980, C:A978
4bpn A5004 2Pout A6024, A6025, A6026, A6027, A6028, A6029 C:A567, A:A1111
4bpo A5048 2Pout A2040, A2041, A2042, A2050, A2411, A2412 A:A108, U:A109
4bpo A5060 2Pout A2134, A2135, A2136, A2211, A2434, A2435 G:A610, A:A609
4bpo A5038 2Pout 42001, 42002, A2194, A2195, A2201, A2399 C:A1023, C:A1039
4bpp A5060 2Pout A7971, A7972, A7973, A7974, A7975, A7976 A:A609, G:A610
4dha A3624 2Pout A4460, A4461, A4462, A4463, A4464 C:A2879, U:A2878
4dha 6102 2Pout A4727, 6202, 6203, 6204, 8203, 8204 C:A2347, U:A2348
4dhb A1811 2Pout A2177, A2178, A2179, A2180, A2181, A2182 G:A438, G:A492
4dhb A1806 2Pout A2156, A2157, A2158, A2159, A2160, A2161 U:A387, A:A59
4dhc B216 2Pout B335, B336, B337, B338, B339, B340 U:B55, A:B25
4dr1 A1710 2Pout A2078, A2079, A2080, A2081 A:A1204, U:A1049
4dr3 A1608 2Pout A1914, A1915, A1916, A1917 U:A652, U:A751
4dr4 A1759 2Pout A2322, A2323, N201, N202 A:A1204, G:A1048
4dr4 A1955 2Pout A2465, A2466, A2467, A2468, A2469 A:A185, G:A190
4dr5 A1812 2Pout A2262, A2263, A2264, A2265, A2266, A2267 G:A438, G:A492
4dr5 A1680 2Pout A2091, A2092, A2093, A2094 G:A371, C:A372
4dr5 A1626 2Pout A1968, A1969, A1970, E303 U:A561, U:A20
4dr6 A1845 2Pout A2535, A2536, A2537, A2538, A2539, A2540 C:A934, U:A1345
4dr6 A1654 2Pout A2136, A2137, A2138, A2139 G:A15, A:A16
4dr7 A1609 2Pout A2019, A2020, A2021, A2022 U:A652, U:A751
4duy J201 2Pout A2301, J301, J302, J303, N202, N203 A:A1188, C:A1189
4dv2 A1793 2Pout A2136, A2137, A2138, A2139 C:A150, G:A168
4dv2 A1830 2Pout A2243, A2244, A2245, A2246, A2247 U:A1345, C:A934
4dv3 A1833 2Pout A2183, A2184, A2185, A2186, J301 C:A972, C:A1366

Site type used in the classification is a string abbreviation of ligand composition in Mg2+ coordination sphere
Abbreviations
used for Mg2+
"Site type"
Mg2+ inner-sphere ligands Geometry for inner-sphere OP Mg2+ outer-sphere moieties
Oph phosphate oxygen (OP1/OP2)
Or ribose oxygen (O2'/O4')
     or oxygen bridging phosphate and ribose (O3'/O5')
Ob nucleobase oxygen      Nb nucleobase nitrogen
cis- two OP ligands adopt cis- isoform
trans- two OP ligands adopt trans- isoform
fac- three OP ligands adopt fac- isoform
mer- three OP ligands adopt mer- isoform
Pout phosphate moiety
Rout ribose moiety
Bout nucleobase moiety
Reference: Zheng H, Shabalin IG, Handing KB, Bujnicki JM, Minor W. (2015) Magnesium binding architectures in RNA crystal structures: validation, binding preferences, classification, and motif detection. Nucleic Acid Research 43(7):3789-801 [Pubmed].


Developed by Heping Zheng and Ivan Shabalin at Minor lab (http://olenka.med.virginia.edu/CrystUVa/)
For any help please contact <dust@iwonka.med.virginia.edu>